Egypt's military ruler Field Marshal Hussein Tantawi contacted Saudi officials to try to mend the rift after the "surprise decision," Egypt's official news agency MENA reported.
SPA said King Abdullah received a call from Tantawi and pledged to examine the issue in the coming days while "trying to take into account the interests of the two countries."
The protests in the Egyptian capital were "unjustified," the official spokesman in Riyadh said, adding that Saudi and Egyptian employees of its diplomatic missions had been threatened.
"Hostile slogans were shouted out and the immunity of the diplomatic representations was violated, contrary to all international regulations," the spokesman said.
He said the violence had led to the suspension of diplomatic and consular services for Egyptian workers and Muslim pilgrims headed for Islam's holiest sites, located in western Saudi Arabia.
Egypt's Al-Ahram quoted an online cabinet statement voicing "its regret over the incidents by some individuals against the embassy of brotherly Saudi Arabia in Cairo, and which only express the opinion of those who carried them out."
It said such "irresponsible actions... harm the deep relations between Egypt and Saudi Arabia."
The daily also reported a statement by the Freedom and Justice Party, political arm of Egypt's powerful Muslim Brotherhood, calling on Saudi Arabia to reconsider.
However, the FJP statement said the protests expressed "Egyptians' will to preserve the dignity of their citizens."
On Tuesday, hundreds of Egyptians protested outside the embassy demanding the release of an Egyptian human rights activist and lawyer held by Saudi authorities who claim he possessed banned drugs.
The protesters chanted slogans against the Saudi regime as they called for the "immediate" release of Ahmed Mohammed al-Gizawi, who was arrested on arrival at Jeddah airport on April 17.
The Arabic Network for Human Rights Information, an Egyptian organisation, said Gizawi was detained following a sentence of one year in prison and 20 lashes delivered against him in absentia for criticism of the Saudi government.
Gizawi, whose supporters said he travelled to the Gulf state on pilgrimage, was being targeted for his activism in favour of Egyptian detainees in Saudi prisons, it said.
Defending compatriots, he had accused King Abdullah and Saudi authorities of arbitrary arrests and torture of Egyptians in the oil-rich country, according to rights groups in Egypt.
They said the lawyer, who had not been informed of his conviction, was travelling with his wife when he was arrested.
Egyptian Foreign Minister Mohammed Kamel Amr has said he instructed the country's embassy in Riyadh "to make urgent contacts with Saudi authorities" to press for the lawyer's release.
But the Saudi ambassador to Cairo, Ahmed Adel Aziz Qattan, in a statement said no jail or whipping sentence had been passed against Gizawi, who had however been stopped in possession of thousands of pills considered a banned drug.
The pills were found concealed in cartons of children's milk and in the covers of two copies of the Koran holy book, according to the ambassador.